The recovery of one of Australia's top diving spots is in doubt after recent wild storms in the Hunter have caused headaches with a natural sand build-up.

Port Stephens Council was forced to remove several thousand tonnes of sand from Shoal Bay in 2010 after a build-up over several months smothered coral and sponges.

Local divers say the area was recovering well, but that is now uncertain after bad weather dragged large volumes of sand into deep water.

Dive shop owner Matt Doyle says while some areas are still full of life, it was not the outcome he was hoping for.

"The big storm systems that we had come through a couple of months ago have gouged a lot of the sand out instead of moving the sand away, as I guess a lot of us hoped, it's literally just dragged it down into the deeper water," he said.

"The site itself was actually recovering quite nicely in areas.

"From what we could see after that particular period of bad weather, I think it's gone two steps backwards again."

Mr Doyle says it is frustrating to watch the world-renowned dive spot struggle to recover.

"It is a little disappointing and I must admit, I did feel a little sad having seen it.

"But at the end of the day, it's what's occurred and we've got to live with it and we just make the best of it as best we can."